Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland

Hindawi Publishing Corporation BioMed Research International Volume 2015, Article ID 979530, 17 pages http://dx.doi.org/10.1155/2015/979530 Research Article Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland Malin Bomberg,1 Mari Nyyssönen,1 Petteri Pitkänen,2 Anne Lehtinen,2 and Merja Itävaara1 1 VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 Espoo, Finland 2Posiva Oy, Olkiluoto, 27160 Eurajoki, Finland Correspondence should be addressed to Malin Bomberg; [email protected] Received 6 January 2015; Accepted 4 March 2015 Academic Editor: Weixing Feng Copyright © 2015 Malin Bomberg et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland) using bacterial and archaeal 16S rRNA, dsrB, and mcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296–798 m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ) at 250–350 m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizing -proteobacteria (Sulfurimonas sp.) dominated in the SMMZ and -proteobacteria (Pseudomonas spp.) below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG) were more common at 415–559 m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea, -, -and-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths. DsrB genes were most numerous and most actively transcribed in the SMMZ while the mcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems. 1. Introduction Deep subsurface microbial communities of the Fenno- scandian Shield, including Olkiluoto, are functionally diverse Stable deep terrestrial subsurface locations are presently and play a role in a variety of redox reactions, such as nitrate, being considered for long-term geological disposal of spent iron, and sulphate reduction, as well as methanogenesis nuclear fuel. Microbe-mediated processes may play a key (e.g., [3–6]). While the presence of these processes has been role in the long-term stability and risk assessments of such confirmed by cultivation based techniques4 [ , 5, 7]andDNA- storage. Dissolved sulphide produced by sulphate reducing based PCR techniques [3, 6, 8], activity of these processes in bacteria (SRB), for example, may exert influence on spent situ remains uncertain. nuclearfuelcanistercorrosionleadingtomobilityofradionu- In general, deep subsurface microbial communities clides [1]. In Olkiluoto, Finland, spent nuclear fuel will be appear to have extraordinarily low metabolic activity [6]. disposed approximately 450 m deep in the bedrock. There- However, under certain environmental conditions, such as fore,understandingtheroleandfunctionalityofmicrobial sulphate-methane transition zones (SMTZ), microbial activ- communities in this environment is of critical importance for ity appears to increase dramatically [9, 10]. At SMTZs in ma- the safety of the spent nuclear fuel repository [2]. rine sediments, concentrations of H2Sincrease(e.g.,[11, 12]) 2 BioMed Research International possibly due to anaerobic oxidation of methane (AOM) and almost 60 boreholes drilled for research and monitoring 2− simultaneous reduction of SO4 . In addition, both microbial purposes and studies on the chemistry and microbiology cell concentration and microbial diversity have been seen to of the groundwater have been on-going since the 1980s be elevated in sedimentary SMTZ environments [10]. Little is [2]. The groundwater in Olkiluoto is stratified relative to known of the activity, function, and composition of microbial physicochemical parameters [18]. From the surface to a depth communities in methane-rich deep terrestrial groundwater of30mbgslthewaterisofmeteoricorigin(i.e.precipitation) or terrestrial groundwater SMMZs. and the water type is fresh to brackish. The uppermost Methane and sulphates are major constituents of Olk- 100 mbgsl has a high concentration of dissolved inorganic iluoto groundwater, residing in different groundwater layers carbon (as bicarbonates), and salinity (as total dissolved [2]. Sulphate-rich water prevails at depths above 300 m solids [TDS] and chlorine) increases with depth. Between below ground surface level (mbgsl) and methane-rich water 100 and 300 mbgsl, salinity is roughly similar to the present dominates below 300 mbgsl. A sulphate-methane mixing day Baltic Sea, but, below 300 mbgsl, the salinity increases −1 zone (SMMZ) can be identified between 250 and 350 mbgsl up to 84 g TDS L at 1000 mbgsl. Based on drill core [2]. In contrast to the clearly identifiable sharp SMTZs logging, the bedrock of Olkiluoto consists mainly of gneiss formed in anaerobic aquatic sediments [13, 14] the SMMZs (9% of the bedrock volume), migmatitic gneiss (64% of the in deep terrestrial groundwater are broad. In deep terrestrial bedrock volume), TGG (tonalite-granodiorite-granite) gneiss subsurface, groundwater resides in bedrock fractures, which (8%), and pegmatitic granite (19%) [19]. In addition, of the may be almost isolated and thereby exhibit stagnant ground- migmatitic gneiss 67% is veined and 33% diatexitic gneiss. 2− water or well connected with each other, which enables Between 100 and 300 mbgsl, the SO4 concentration is different degrees of groundwater flow. In addition, strong elevated in ancient (i.e., pre-Baltic) seawater derived ground- environmental changes, such as infiltration of surface water, water. Below this layer, the methane concentration in the − 2− crustal rebound, glaciation or deglaciation can affect the water increases and Cl dominates whereas SO4 is almost stability and position of the SMMZ [15]. absent. A mixing zone where methane-rich groundwater Recently Pedersen et al. [16] simulated SMMZ mixing diffuses into sulphate-rich groundwater (a sulphate-methane effect in Olkiluoto groundwater. By gradually increasing the mixing zone, SMMZ) can be identified at 250 to 350 mbgsl concentration of sulphate in methane-rich and sulphate-poor depth. This zone is characterized by increased concentration groundwater over an experimental period of 103 days, the of sulphide and a decrease in sulphate and methane. ∘ authors showed that the composition of the microbial com- The temperature rises linearly with depth, from ca. 5-6 C ∘ munity was strongly influenced by sulphate and methane. at 50 mbgsl to ca. 20 C at 1000 mbgsl [20]. The pH of the Several studies in Olkiluoto also show that the microbial water is slightly alkaline throughout the depth profile. Several communities in Olkiluoto groundwater are stratified and aquifer zones, such as zones HZ20 or HZ21, span several potentially affected by the groundwater SMMZ [3, 6, 17]. different boreholes (Table 1). -and-proteobacteria are generally found in water layers aboveandintheSMMZwhile -proteobacteria become more 2.2. Sampling. Deep groundwater samples (Table 1)from abundant in the deeper methane-rich water [3, 6]. A clear specific fracture zones were collected from seven different increase in the number of methanogens was also detected boreholes in Olkiluoto (Figure 1) between December 2009 simultaneously with a decrease in the number of sulphate and May 2010. Fracture zones were isolated by permanent reducing bacteria (SRB) in Olkiluoto deep groundwater [3, or temporary inflatable packers as described previously [3]. 17]. In addition, analysis of methyl coenzyme M reductase Packer-sealed fracture zones were purged by pumping for (mcrA) gene clone libraries demonstrates the presence of at least four weeks prior to sampling in order to allow putative anaerobic methane oxidizing group 1 (ANME-1) indigenous fracture water to fill the isolated borehole section. archaea at 300–400 m depth [3]. Here, we extend this research and use RNA-targeted Anaerobic groundwater was pumped from the borehole high-throughput (HTP) sequencing to investigate the active directly in to an anaerobic chamber (MBRAUN, Germany) SRB and methanogen communities of the methane-rich deep through a sterile, gas-tight polyacetate tube (8 mm outer groundwater around the depth of the nuclear waste reposi- diameter), where samples were collected in acid-washed, tory rising up in to the SMMZ at the Olkiluoto site. In order sterile2LSchottglassbottles(DuranGroupGmBH,Ger- to study the active microbial community in fracture water many). Microbial biomass for nucleic acid analyses was samples, the bacterial and archaeal 16S rRNA pools were also concentrated from 500 mL and 1000 mL samples by vacuum characterized and used as proxy for active (living) microbial filtration through cellulose acetate membranes (0.2 mpore cells. In addition, the abundance of SRB and methanogen size, Corning, MA, USA) inside the glove box. Filters

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